Contacts of the strand formed by residues 30 - 37 (chain C) in PDB entry 1NQ3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 30 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 4.4 7.7 + - - +
25C VAL 3.5 1.9 - - - +
26C LEU* 3.5 1.3 - - - -
27C VAL* 2.9 36.1 + - - +
28C ASP* 5.6 0.7 - - - +
29C ARG* 1.3 80.6 + - - +
31C ILE* 1.3 63.7 + - - +
32C TYR* 3.7 32.9 + - + +
126C ILE* 3.9 22.2 - - + -
127C ALA 3.5 4.7 - - - +
128C VAL* 4.4 10.8 - - + +
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Residues in contact with ILE 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 4.9 4.9 - - + -
24C ALA* 4.1 14.6 - - + -
25C VAL 3.5 8.1 - - - +
26C LEU* 3.8 20.9 - - + -
29C ARG 4.5 3.6 - - - +
30C THR* 1.3 75.7 - - - +
32C TYR* 1.3 61.8 + - - +
33C ILE* 3.7 23.1 + - + +
65C ILE* 5.6 1.1 - - + -
66C LEU* 5.2 2.7 - - + -
69C ALA* 3.6 30.1 - - + +
71C CYS* 3.7 23.3 - - + -
125C ALA 4.0 0.2 - - - +
126C ILE* 3.3 7.6 - - - +
127C ALA* 2.6 48.9 + - + +
129C GLN* 4.7 6.3 - - + +
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Residues in contact with TYR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 4.6 6.0 + - - -
30B THR* 4.5 9.7 + - - +
32B TYR* 4.5 6.4 + - - -
77B VAL* 3.9 21.5 - - + +
78B LYS* 4.0 26.7 - - + +
106B ALA* 3.3 16.5 - - + +
126B ILE* 3.8 36.5 - - + +
128B VAL* 5.5 1.4 - - + +
24C ALA* 3.2 3.5 - - - -
25C VAL 2.9 36.6 + - - +
27C VAL* 3.7 25.1 - - + -
30C THR* 3.7 24.3 - - + +
31C ILE* 1.3 72.9 - - - +
33C ILE* 1.3 62.0 + - - +
125C ALA 4.2 2.5 - - - -
126C ILE* 4.2 26.0 - - + -
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Residues in contact with ILE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LYS* 4.3 8.0 - - - +
106B ALA* 4.3 2.2 - - - -
23C GLN 3.8 10.3 - - - +
24C ALA* 4.1 5.2 - - + -
31C ILE* 3.8 19.3 - - + +
32C TYR* 1.3 74.8 - - - +
34C SER* 1.3 75.4 + - - +
35C GLY 3.7 1.0 + - - -
36C GLN* 4.6 4.7 - - + -
62C ILE* 4.4 13.9 - - + -
65C ILE* 4.2 22.7 - - + -
66C LEU* 3.6 35.0 - - + -
124C GLU* 3.9 4.5 - - - +
125C ALA* 3.0 47.4 + - + +
127C ALA* 4.6 5.4 - - + -
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Residues in contact with SER 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LYS* 5.2 0.2 - - - +
106B ALA* 3.3 3.0 - - - +
107B ARG 2.8 35.0 + - - +
21C TYR* 3.4 17.3 - - - -
22C SER 2.5 26.0 + - - -
23C GLN 2.9 16.7 + - - -
33C ILE* 1.3 79.0 - - - +
35C GLY* 1.3 66.0 + - - +
36C GLN* 3.2 21.3 + - - +
123C ILE 4.0 1.6 - - - +
124C GLU* 4.5 0.2 - - - -
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Residues in contact with GLY 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG 3.1 14.0 + - - +
108B ALA* 4.4 1.7 - - - +
21C TYR* 5.5 2.9 - - - -
33C ILE 3.7 1.6 + - - -
34C SER* 1.3 74.7 - - - +
36C GLN* 1.3 65.3 + - - +
37C LEU* 4.2 1.9 + - - +
122C GLU* 3.5 26.1 - - - +
123C ILE 3.4 9.9 - - - -
124C GLU* 3.7 14.9 - - - +
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Residues in contact with GLN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PRO* 3.9 23.8 + - - +
21C TYR* 5.6 2.1 - - - -
23C GLN* 4.3 4.7 - - - +
33C ILE* 4.6 0.7 - - + -
34C SER* 3.2 27.2 - - - +
35C GLY* 1.3 78.2 - - - +
37C LEU* 1.3 63.2 + - - +
39C MET* 5.6 2.8 - - - +
58C ALA* 3.7 24.3 - - - +
61C ASN* 3.8 18.0 + - + +
62C ILE* 3.7 20.4 - - + -
65C ILE* 3.5 27.4 - - + +
122C GLU* 3.3 6.6 - - - -
123C ILE 2.8 35.7 + - - +
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PRO* 5.1 0.3 - - - +
35C GLY 4.2 1.5 + - - +
36C GLN* 1.3 78.6 + - - +
38C GLY* 1.3 59.4 + - - +
39C MET* 2.8 45.7 + - + +
46C LEU* 4.3 5.8 - - + -
54C GLU* 6.1 0.2 - - - +
58C ALA* 3.6 6.7 - - - -
61C ASN* 3.2 15.6 - - - +
115C LEU* 4.4 5.6 - - + -
116C PRO* 3.7 43.1 - - + +
117C LYS* 4.6 7.9 - - + -
119C GLY* 4.8 5.2 - - - -
121C VAL 3.7 11.0 - - - +
122C GLU* 3.5 38.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il